The invention discloses a fish ultrasonic wave marker precise positioning method and system suitable for a complex water environment. The method comprises the steps of S1, collecting the time when a signal marker fish arrives at each hydrophone in a hydrophone monitoring network or the time difference between arrivals at two hydrophones; S2, estimating approximate coordinates and a signal emissiontime of the signal marker fish by using a Chan algorithm; S3, taking the approximate coordinates of the signal marker fish as the center, constructing an approximate coordinate alternative interval,and dividing the approximate coordinate alternative interval into sub-nets; S4, taking a node position of one subnet as a position initial value of the signal marker fish, and carrying out the signalmarker positioning calculation by using the robust least-square estimation; and S5, evaluating a positioning calculation result obtained in the step S4, if the evaluation passes, determining the position calculation result as the precise positioning result of the signal marker fish, and otherwise, repeating the step S4. The method of the invention can effectively realize the accurate capture of fish movement trajectories with high precision and high reliability.